# This is the Makefile for testing the secondary structure predictor
# predict-2nd
2ND = /projects/compbio/usr/cbarrett/predict-2nd
2ND-TESTING = ${2ND}/testing
QUALITY-REPORTS = ${2ND-TESTING}/quality-reports
RUN-SCRIPTS = ${2ND-TESTING}/run-scripts
NETS = ${2ND-TESTING}/networks
LOGS = ${2ND-TESTING}/logs
TRAINING-DATA = ${2ND-TESTING}/training-data
PLOTS = ${2ND-TESTING}/plots
SCRIPTS = ${2ND-TESTING}/scripts

.PHONY: default clean-tests clean-logs %-both.quality
.PRECIOUS: ${QUALITY-REPORTS}/%.quality ${QUALITY-REPORTS}/%-both.quality \
	   %.quality  %.script %.net
.DELETE_ON_ERROR: %.script %.net


# Training data sets
test = ${TRAINING-DATA}/test.training-data
phdset = ${TRAINING-DATA}/phdset.training-data



default:
	@echo There is no default behavior for this makefile

# Need to figure out a way to incorporate error checking into this
%.script: 
	@echo "Creating $@";\

	@echo "ReadNeuralNet ${NETS}/$*.net" > ${RUN-SCRIPTS}/$@
	@echo "" >> ${RUN-SCRIPTS}/$@

	@if echo $* | egrep -q comp;\
	then \
	  echo "WeightingRegularizer /projects/compbio/lib/recode2.20comp" \
	        >> ${RUN-SCRIPTS}/$@;\
	  echo "SequenceWeight EntropyWeight 1.0 10.0" >> ${RUN-SCRIPTS}/$@;\
	  echo "ReRegularizer  /projects/compbio/lib/recode2.20comp" \
	        >> ${RUN-SCRIPTS}/$@;\
	  echo "" >> ${RUN-SCRIPTS}/$@;\
	fi

	@echo "ReportNetQualityForCrossTrainTo ${QUALITY-REPORTS}/$*.quality" \
	       >> ${RUN-SCRIPTS}/$@
	@echo "" >> ${RUN-SCRIPTS}/$@

	@echo "ReportNetQualityForTrainTo ${QUALITY-REPORTS}/$*-t.quality" \
	       >> ${RUN-SCRIPTS}/$@
	@echo "" >> ${RUN-SCRIPTS}/$@

	@if echo $* | egrep -q test;\
	then \
	   cat ${test} >> ${RUN-SCRIPTS}/$@;\
	elif echo $* | egrep -q phdset;\
	then \
	   cat ${phdset} >> ${RUN-SCRIPTS}/$@;\
	else \
	   echo "ERROR: Don't know what training set in ${TRAINING-DATA}\
	          to use for $@";\
	fi

	@echo "" >> ${RUN-SCRIPTS}/$@
	@echo "TrainNet 200" >> ${RUN-SCRIPTS}/$@
	@echo "ReportNeuralNet ${NETS}/$*-trained.net" >> ${RUN-SCRIPTS}/$@
	@echo "Quit" >> ${RUN-SCRIPTS}/$@


${QUALITY-REPORTS}/%-both.quality: %-aa.quality %-comp.quality
	@echo "Making $^"

${QUALITY-REPORTS}/%.quality: %.script %.net
	${2ND}/predict-2nd < ${RUN-SCRIPTS}/$< 

%.quality: ${QUALITY-REPORTS}/%.quality
	@echo "Making $^"

%.net: ${SCRIPTS}/make-network
	@echo "Creating ${NETS}/$*.net"
	@${SCRIPTS}/make-network $* > ${NETS}/$*.net



clean-logs:
	rm -f ${LOGS}/*

clean-tests:
	rm -f ${2ND-TESTING}/*/test*

#
# The following targets are for creating gnuplot plots
#
all-onelayer-%-q3.ps: ${QUALITY-REPORTS}/phdset-5-3-%.quality \
		${QUALITY-REPORTS}/phdset-7-3-%.quality \
		${QUALITY-REPORTS}/phdset-9-3-%.quality \
		${QUALITY-REPORTS}/phdset-11-3-%.quality \
		${QUALITY-REPORTS}/phdset-13-3-%.quality \
		${QUALITY-REPORTS}/phdset-15-3-%.quality \
		${QUALITY-REPORTS}/phdset-17-3-%.quality \
		${QUALITY-REPORTS}/phdset-19-3-%.quality 
	@echo 	Creating $@
	@echo 	set ylabel \"Q3\"\; \
		set xlabel \"Iteration\"\; \
		set yrange \[.4\:.75\]\; \
		set title \"all onelayer-$*-q3 for different window sizes\"\; \
		set data style lines\; \
		set term postscript color\; \
		set output \"${PLOTS}/$@\"\; \
		plot \"${QUALITY-REPORTS}/phdset-7-3-$*.quality\" \
			using 3 title \"7\"\, \
		\"${QUALITY-REPORTS}/phdset-9-3-$*.quality\" \
			using 3 title \"9\"\, \
		\"${QUALITY-REPORTS}/phdset-11-3-$*.quality\" \
			using 3 title \"11\"\, \
		\"${QUALITY-REPORTS}/phdset-13-3-$*.quality\" \
			using 3 title \"13\"\, \
		\"${QUALITY-REPORTS}/phdset-15-3-$*.quality\" \
			using 3 title \"15\"\; quit | gnuplot


%-both.ps: ${QUALITY-REPORTS}/%-aa.quality ${QUALITY-REPORTS}/%-comp.quality

%-q3.ps:	${QUALITY-REPORTS}/%.quality
	@echo   Creating $@
	@echo 	set ylabel \"Q3\"\; \
		set xlabel \"Iteration\"\; \
		set yrange \[0\:1\]\; \
		set title \"$*-q3\"\; \
		set data style lines\; \
		set term postscript color\; \
		set output \"${PLOTS}/$@\"\; \
		plot \"${QUALITY-REPORTS}/$*.quality\" using 3 title \"Q3\"\; \
		quit | gnuplot

%-rms.ps:	${QUALITY-REPORTS}/%.quality
	@echo   Creating $@
	@echo 	set ylabel \"RMS\"\; \
		set xlabel \"Iteration\"\; \
		set title \"$*-rms\"\; \
		set data style lines\; \
		set term postscript color\; \
		set output \"${PLOTS}/$@\"\; \
		plot \"${QUALITY-REPORTS}/$*.quality\" using 8 title \
		\"rms_sum\"\, \"${QUALITY-REPORTS}/$*.quality\" \
		using 9 title \"rms_weight\"\; \
		quit | gnuplot

%-rms-q3.ps:	${QUALITY-REPORTS}/%.quality
	@echo   Creating $@
	@echo 	set logscale y \; \
		set ylabel \"RMS and Q3\"\; \
		set xlabel \"Iteration\"\; \
		set title \"$*-rms-q3\"\; \
		set data style lines\; \
		set term postscript color\; \
		set output \"${PLOTS}/$@\"\; \
		plot \"${QUALITY-REPORTS}/$*.quality\" using 8 title \
		\"rms_sum\"\, \"${QUALITY-REPORTS}/$*.quality\" \
		using 9 title \"rms_weight\"\, \
		\"${QUALITY-REPORTS}/$*.quality\" using 3 title \
		\"Q3\"\; \
		quit | gnuplot

%-rates.ps:	${QUALITY-REPORTS}/%.quality
	@echo   Creating $@
	@echo 	set ylabel \"Rates\"\; \
		set xlabel \"Iteration\"\; \
		set title \"$*-rates\"\; \
		set data style lines\; \
		set term postscript color\; \
		set output \"${PLOTS}/$@\"\; \
		plot \"${QUALITY-REPORTS}/$*.quality\" using 10 title \
		\"WeightRate\"\, \"${QUALITY-REPORTS}/$*.quality\" \
		using 11 title \"PseudoRate\"\; \
		quit | gnuplot

%-q3-both.ps:	${QUALITY-REPORTS}/%-aa.quality \
		${QUALITY-REPORTS}/%-comp.quality
	@echo   Creating $@
	@echo 	set ylabel \"Q3\"\; \
		set xlabel \"Iteration\"\; \
		set yrange \[0\:1\]\; \
		set title \"$*-q3-both\"\; \
		set data style lines\; \
		set term postscript color\; \
		set output \"${PLOTS}/$@\"\; \
		plot \"${QUALITY-REPORTS}/$*-aa.quality\" using 3 title \
		\"aa\"\, \"${QUALITY-REPORTS}/$*-comp.quality\" \
		using 3 title \"comp\"\; \
		quit | gnuplot